


In Accordance with Cole Protocol, Article 2

by YappiChick



Category: Halo
Genre: Alternate Ending, Gen
Language: English
Status: Completed
Published: 2013-01-11
Updated: 2013-01-11
Packaged: 2017-11-25 03:38:39
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 2,660
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/634712
Author URL: https://archiveofourown.org/users/YappiChick/pseuds/YappiChick
Summary: <blockquote class="userstuff">
              <p>John wasn't going to leave her that with that...Gravemind.</p>
            </blockquote>





	In Accordance with Cole Protocol, Article 2

**Author's Note:**

> So, I have issues with the ending of Halo 2. Though I do appreciate what came from it (mainly "Human Weakness" and the "Cortana" cutscene), I thought the idea of leaving Cortana behind was a plot device to create angst in Halo 3 (It was.) and there were some big, huge emergency exits that Bungie could have had Cortana taken but, again, Angst!! So, this is my take on the end. You're in official AU territory. You've been warned.
> 
> There are major references to First Strike, but really, you don't need to have read it to understand the story. Kudos and praise to Halopedian for having the Halo 2 transcript; quotes from the level are used throughout the fic.

Truth was headed towards Earth.  
  
As Mercy lay before him, withering as the last of his life drained from him, the Chief knew what they had to do: protect humanity from another attack by a Covenant Prophet.  
  
Cortana's avatar appeared on the top of Truth’s fallen throne. Her lips were turned down in a frown. "That structure, at the center of the city..." She paused for a second before a stricken look passed over her face. "...it's a Forerunner Ship! And Truth is heading straight for it! If he leads the Covenant fleet to Earth, they won't stand a chance. You have to stop him."  
  
There was a tension in Cortana’s voice that mirrored John's concern. This was like Reach all over again.  
  
But this time, the stakes were much, much higher. He faced Cortana, looking away from Mercy. "That Brute has the Index. And Miranda and Johnson. He can activate the ring."  
  
Cortana nodded as she crossed her arms. "If he does, I'll detonate _In Amber Clad_ 's reactor just like we did the Autumn's. The blast will destroy this city and the ring.” Her brow furrowed. “Not a very _original_ plan, but we know it'll work."  
  
John gave a curt nod before reaching out to take Cortana with him. To his surprise, she didn’t transfer herself out of _High Charity_ ’s systems. In fact, she pulled away slightly from his hand. "No. I don't want to chance a remote detonation. I'll need to stay here."  
  
He stepped away from the plinth reluctantly, not liking her idea. But, his argument was cut short when a Pelican crashed into the platform behind them. His fingers wrapped tighter around the handle of his gun as he watched the Flood pour out of the ship and into the city they were stranded in.  
  
It was time to fight.  
  
Still, he had to be certain. He faced Cortana again. “Are you sure?”  
  
The AI shrugged. “As sure as I’ll ever be. Besides, I’m safer in here than I am gallivanting around with you. I don’t think AIs are as tasty as humans to the Flood.” She punctuated her statement with a smirk.  
  
Without a counterargument, he was forced to step away from Cortana, despite his lingering unease.  
  
He had barely moved from the fallen Marcy and Cortana when the Flood started to attack. He dropped his expended Carbine and grabbed a energy sword that was lying on the ground. He stabbed at the infection forms that were launching themselves at him. Cautiously, he took a step back as their pus-filled bodies exploded.  
  
He continued making his way through the twisted bowels of the city, dodging the Flood and Covenant as best he could. The Energy Sword, while powerful, was also burdensome for the Spartan.  
  
He turned a corner and walked through another room to a set of doors. They opened, revealing a fallen Brute that was being consumed by a pair of infection forms. John carefully snagged a plasma rifle that was several feet away and continued making his way to the waypoint Cortana had marked on his HUD.  
  
Cortana’s voice cut across their comm channel. “"Flood controlled-dropships are touching down all over the city! That creature beneath the Library... that 'Gravemind'... used us. We were just a diversion. _In Amber Clad_ was always its intended vector.” Annoyance laced her speech. “There's a conduit connecting this tower to the ship. Head back inside. I'll lead you to it."  
  
As he made his way through the bowels of _High Charity_ and watched the consumption of the Covenant around him, John knew there was no way he was going to leave Cortana on this Flood-invested “holy” city of the Prophets.  
  
John was tempted to begin voicing his opposition to her plan to stay behind, but he had more pressing matters to pay attention to, like the infected Brute that was attempting to blow a hole in his helmet with a plasma cannon. He fired a barrage of shots into the creature before clearing the rest of the room.  
  
Decades of fighting taught the Chief to be patiently ruthless against a seemingly unending enemy. His aim was perfect; his determination unwavering. Finally, he reached the lift at the end of the hall.  
  
He stepped on and looked up, ready for any Flood to jump in his direction in an attempt to devour him. The lift slowly rose to the next level.  
  
While the Master Chief focused on the primary mission of stopping Truth before he was able to flee, a small recess of John’s mind was still busy trying to figure out how to accomplish his secondary mission: to convince Cortana to come with him back to Earth.  
  
"I'll disable this lift once you reach the top. That'll slow them down...I hope."  
  
He heard the uncertainty in her voice. A feeling of unease settled over him; Cortana rarely sounded overwhelmed. If she was concerned, he knew to be on alert as well.  
  
His grip on the plasma rifle tightened as the lift started to rise. “Cortana, I’m not--”  
  
He was cut off as the lift stopped and another voice slithered over the ship’s speakers. “Shall we let the Flood consume our holy city? Turn _High Charity_ into another of their wretched hives? No enemy has ever withstood our might. The Flood too shall fail."  
  
Truth.  
  
The desire to talk Cortana about her plan to remain on _High Charity_ was shoved aside by John’s resolve to find the fleeing Prophet while the faithful remained to fight a doomed fight against the Flood. He sprinted ahead, determined to stop Truth before he left for Earth.  
  
“You’ve got to stop his ship from leaving,” he said to Cortana as he ducked behind a wall, dodging a shot from a Brute.  
  
"I'll do what I can to slow the launch sequence, but there's something inside the ship...” She paused briefly. “...a presence that's fighting back. For a Covenant construct, it's unusually formidable." He could almost feel her frowning, despite the fact she was still in _High Charity_ ’s systems.  
  
His brow furrowed. Cortana had been able to hack into the Halo's control systems and circumvent the Index from being activated. What AI could the Covenant have acquired that could thwart Cortana?  
  
“Don’t worry, Chief," she said not quite convincingly, "it’s nothing I can’t handle.”  
  
The swarms of Flood that were scurrying across the floor, walls and ceilings underscored the fact that both of them were in situations they could hardly handle.  
  
"Cortana--" _Be careful._ "--Keep me posted about Truth's movements."  
  
There was a half-second pause. John wondered if she was preoccupied with circumventing the Covenant construct. But when she spoke and John heard the softness in her voice, he knew she heard his unspoken words. "I will, Chief."  
  
He cautiously proceeded through the darkened hall, eliminating any threat --Covenant or Flood-- that got in his way. When he got to another set of doors, he swapped out his rifle for another discarded one that was laying next to a dead Elite. Then, he stepped in front of the door and entered into the large room that was before him.  
  
Inside, the Covenant were continuing to make their feeble attempt combat the Flood, but they were fighting a losing battle. That didn’t stop the Covenant from taking aim at the Spartan as he walked through the room. He dodged several shots before raising his pistol.  
  
Before he could fire, John watched as a group of infection forms dart across the floor, escaping the brunt of the Covenant’s attack, and latched itself on a Brute. He paused for a precious second as he watched the Brute transform into an abomination of its former self.  
  
Then, John fired, killing the infected Covenant.  
  
As he stepped by the twitching body, he double downed on his promise to himself that Cortana would not remain here.  
  
He made his way through the room when he heard Truth speak to his followers, urging them to remain in a battle he was unwilling to fight on his own. Then, a voice --the voice of the Gravemind-- cut across the speakers.  
  
"Arrogant creature! Your deaths will be instantaneous, while we shall suffer the progress of infinitude!"  
  
“Charming,” Cortana muttered. “I’m sure he’ll make pleasant company for me.”  
  
John didn’t bother to argue with Cortana. Yet. The firefight around him was too intense for him to engage in a battle of wills with the one person who rivaled his own stubbornness.  
  
He needed to come up with a convincing argument or he knew he would lose the fight.  
  
There had to be a way to persuade her to leave _High Charity._  
  
A plasma grenade shook the floor, pulling him from the thoughts of Cortana. Bodies of exploding flood parasites flew in the air.  
  
John moved forward.  
  
He crept in the shadows as the fighting continued. Cortana warned him about the strength of the security systems and the Gravemind and Truth had another exchange, but John was too busy keeping himself alive to give either much notice.  
  
The Flood were busy taking over the city. It wouldn’t be long before the Covenant would be overrun. Somehow John was sure that Truth would make sure he was off _High Charity_ with plenty of time to save his life.  
  
He rode up another lift as Cortana’s voice cut across his channel. "Apparently, these are the Prophet Hierarchs' private quarters. Their inner sanctum."  
  
“Have you been able to disable the Covenant AI?” he asked as he rode upwards.  
  
“No.” The annoyance was palpable. “I’m not giving up though.”  
  
More fighting greeted John as he stepped off the lift. Flood were consuming Covenant. Covenant were fighting as best they could.  
  
It wasn’t enough.  
  
"Brute and Elite ships are engaging one another all around _High Charity_. I'm running out of options, Chief. I can't stall the launch sequence much longer.” The gnawing concern John had been feeling deepened. If Truth had an AI that was more powerful than Cortana, Earth was in more trouble than he thought.  
  
Cortana continued, “The next lift will take you up to the conduit. Hurry!"  
  
Silently, he rode up the lift. He started to mentally prepare himself for the next, more important confrontation that lay ahead for him: convincing Cortana to get on Truth’s ship with him. Cortana would put up a fight, but John had battled against forces that were more formidable than her.  
  
Or, at least, that’s what he told himself.  
  
When the lift stopped, the Flood were waiting for him, ready to attack. He ducked behind the columns as he aimed towards the upper level. He quickly swapped his plasma rifle for an energy sword and slashed the Flood that were rushing towards him.  
  
He could barely hear Cortana’s voice over the attack. "I knew the Covenant were good at re-purposing Forerunner technology, but this is amazing...” Her voice trailed off. “They've been using the Forerunner ship's engines as an energy source for the city. The ship isn't so much launching as it is disengaging; uncoupling itself from _High Charity_ 's power grid - Stopping Truth, that's all that matters!"  
  
He disagreed. But as a tentacle from an infected Brute came rushing towards him, his opposition was silenced.  
  
He attacked the remaining Flood, snagging another dropped plasma rifle.  He took aim at the Jackal on the ridge and fired.  
  
Chest heaving, he ran up the ramp to where Cortana was, hand on hip. "You know the plan - You've got to catch Truth, I've got to handle the Index. Go!"  
  
“No.” His one word was more powerful than the rifle in his hand.  
  
Cortana was momentarily stunned into silence.  
  
The Chief turned his attention back to the Flood that were overtaking the room again. With a healthy dose of determination and the plasma rifle in his hand, he disposed of the wave of enemies while Cortana tried to formulate a response.  
  
When there was a break in the onslaught of Flood, Cortana turned to him with her arms crossed. “What do you mean ‘no’?”  
  
“I mean, no,” John said. “Capture of a UNSC AI is unacceptable.” The words of Jacob Keyes’ were fresh in his mind.  
  
“Are you quoting Cole Protocol, Article two?” Cortana asked. “You _do_ realize I’m not a shipboard AI any longer, right?”  
  
“You still have all the knowledge of a shipboard AI,” he countered.  
  
“I have _more_ knowledge than any shipboard AI,” she replied, eyebrow raised. “But, that’s not the point.”  
  
“You’re not staying with that Gravemind,” he said firmly.  
  
She shook her head. “I am flattered by your protectiveness, Chief, but I can’t go with you.” Then, more softly, “Not this time.”  
  
“If the Flood capture you...” As if on cue, another horde of them entered through the door across the room. “...they could find Earth. Then, the Covenant would be the least of our troubles.”  
  
Cortana remained unconvinced. “I hope you’re not questioning my ability to evade capture. Besides,” she said with a sigh, “it won’t take them long to figure it out. Once Mercy is consumed, the Gravemind will know everything he does. Including Earth’s location.”  
  
John didn’t care about what happened to Mercy. He _did_ care about Cortana not remaining with that...creature. He may not be able to plead with her based on emotions of protectiveness that he was unwilling to acknowledge, but he could cite rules and regulations to her. “The Cole Protocol is still in effect,” he gritted.  
  
She shook her head, still unmoved by his argument. “We don’t have time for this, Chief. You need to go now!”  
  
He could be as stubborn as she was.  He didn’t move, except to give a curt shake of his head. “I’m not leaving you behind.”  
  
She looked pained for a moment. “I have to stay here, Chief,” she pleaded. “Please.”  
  
The Flood were quickly approaching where he stood. A quick glance at his HUD told him that he was running out of ammo. Soon, if he couldn’t convince Cortana to transfer herself out of the systems, the Flood were going to engulf them.  
  
Finally, his subconscious offered him a solution that would satisfy Cortana’s need to be able to detonate the reactor and John’s desire to get her on Truth’s ship.  
  
“You could make a clone of yourself,” he rumbled. “She could stay behind and detonate _In Amber’s Clad_ ’s reactor if necessary.”  
  
Cortana paused for a millisecond as she considered his suggestion. “That could work,” she said slowly. “Give me a second.” She closed her eyes for a moment. Then, she opened one eye and looked at him. “You really live by the ‘leave no one behind’ motto, don’t you?”  
  
He didn’t reply.  
  
Moments later, another Cortana appeared next to her. “Done.”  
  
The clone looked at same as the AI, but John thought the duplicate looked slightly dimmer than his Cortana.  
  
“She’ll be able to detonate the reactor without a problem if the Index gets activated.” She looked at the clone up and down. “I’ve stripped her of everything but the most rudimentary programming. I doubt she even knows her own name, but after all the trouble the clones created on the _Unyielding Hierophant_ , I thought I shouldn’t take any unnecessary chances.”  
  
John nodded. “Are you--”  
  
A blast from behind them cut off his question.  
  
“Ready to go?” Cortana finished. “Yes.” She gave the other hologram another look. “Good luck.”  
  
The clone gave her a curt nod. “And to you, CTN 0452-9.”  
  
Cortana rolled her eyes. “I know her personality doesn’t take after me. Maybe she inherited that from you. I _have_ been in that head of yours for a while.” She gave John an uncertain look. “Yank me, Chief.”  
  
Without hesitation, John reached over and transferred Cortana into his armor. A rush of coolness poured over his mind as she interfaced with him. “I hope you know what you’re doing,” she said doubtingly.  
  
He jumped head first into the conduit confidently. “Yeah. We’re finishing this fight. Together.”


End file.
